Structural landscape of the host antiviral restriction factor SAMD9
摘要
Signal Transduction ATPases with Numerous Domains (STAND) proteins function as nucleotide-regulated molecular switches that undergo conformational transitions and higher-order assembly to govern innate immunity. Sterile alpha motif domain-containing 9 (SAMD9), an antiviral restriction factor within the STAND family linked to severe human inflammatory and hematological disorders, lacks a defined structural framework, and whether it follows canonical STAND activation principles remains unknown. Here, we present high-resolution cryo-electron microscopy structures of the human SAMD9 catalytic and regulatory core across multiple conformational and oligomeric states. These structures reveal that SAMD9 exists as a dynamic structural ensemble, comprising a compact autoinhibited monomer, C2-symmetric dimers, asymmetric assemblies, and higher-order oligomers. The monomeric state is pre-loaded with ATP yet remains conformationally restrained by an extensive SIR2–NOD–TPR interaction network, demonstrating that nucleotide occupancy alone is insufficient for activation. Reciprocal NOD-mediated dimerization preserves this autoinhibited architecture, whereas alternative SIR2-mediated assembly modes drive distinct interprotomer interface remodeling and local domain rearrangements. Biochemical analyses demonstrate that although the OB domain contributes to nucleic-acid recognition, nucleic-acid binding alone is insufficient to relieve autoinhibition. Mapping disease-associated variants onto these structures unveils multiple regulatory layers susceptible to pathogenic perturbation. Together, our findings define SAMD9 as a conformationally and oligomerically plastic STAND immune regulator, providing a structural framework to understand its antiviral function and disease-associated pathogenesis.
参考文献
Lee, H. et al. Diverse bacterial pattern recognition receptors sense the core phage proteome. Nature (2026). https://doi.org/10.1038/s41586-026-10852-6
Leipe, D.D., Koonin, E.V. & Aravind, L. STAND, a class of P-loop NTPases including animal and plant regulators of programmed cell death: multiple, complex domain architectures, unusual phyletic patterns, and evolution by horizontal gene transfer. Journal of molecular biology 343, 1–28 (2004).
Koonin, E. & Aravind, L. Origin and evolution of eukaryotic apoptosis: the bacterial connection. Cell Death & Differentiation 9, 394–404 (2002).
Gao, L. et al. Diverse enzymatic activities mediate antiviral immunity in prokaryotes. Science 369, 1077–1084 (2020).
Riedl, S.J., Li, W., Chao, Y., Schwarzenbacher, R. & Shi, Y. Structure of the apoptotic protease-activating factor 1 bound to ADP. Nature 434, 926–933 (2005).
Zhou, M. et al. Atomic structure of the apoptosome: mechanism of cytochrome c- and dATP-mediated activation of Apaf-1. Genes & development 29, 2349–2361 (2015).
Hu, Z. et al. Crystal structure of NLRC4 reveals its autoinhibition mechanism. Science 341, 172–175 (2013).
Zhang, L. et al. Cryo-EM structure of the activated NAIP2-NLRC4 inflammasome reveals nucleated polymerization. Science 350, 404–409 (2015).
Hu, Z. et al. Structural and biochemical basis for induced self-propagation of NLRC4. Science 350, 399–404 (2015).
Wang, J. et al. (2019).
Wang, J. et al. Ligand-triggered allosteric ADP release primes a plant NLR complex. Science 364, eaav5868 (2019).
Gao, L.A. et al. Prokaryotic innate immunity through pattern recognition of conserved viral proteins. Science 377, eabm4096 (2022).
Mekhedov, S.L., Makarova, K.S. & Koonin, E.V. The complex domain architecture of SAMD9 family proteins, predicted STAND-like NTPases, suggests new links to inflammation and apoptosis. Biology direct 12, 13 (2017).
Lemos de Matos, A., Liu, J., McFadden, G. & Esteves, P.J. Evolution and divergence of the mammalian SAMD9/SAMD9L gene family. BMC evolutionary biology 13, 121 (2013).
Xiang, Y. Poxvirus host-range determinants: SAMD9/9L and beyond. Annual review of virology 12, 93–114 (2025).
Liu, J. & McFadden, G. SAMD9 is an innate antiviral host factor with stress response properties that can be antagonized by poxviruses. Journal of virology 89, 1925–1931 (2015).
Zhang, F. et al. Human SAMD9 is a poxvirus-activatable anticodon nuclease inhibiting codon-specific protein synthesis. Science Advances 9, eadh8502 (2023).
Liu, J., Wennier, S., Zhang, L. & McFadden, G. M062 is a host range factor essential for myxoma virus pathogenesis and functions as an antagonist of host SAMD9 in human cells. Journal of virology 85, 3270–3282 (2011).
Meng, X. et al. A paralogous pair of mammalian host restriction factors form a critical host barrier against poxvirus infection. PLoS pathogens 14, e1006884 (2018).
Meng, X., Krumm, B., Li, Y., Deng, J. & Xiang, Y. Structural basis for antagonizing a host restriction factor by C7 family of poxvirus host-range proteins. Proceedings of the National Academy of Sciences 112, 14858–14863 (2015).
Sivan, G., Ormanoglu, P., Buehler, E.C., Martin, S.E. & Moss, B. Identification of restriction factors by human genome-wide RNA interference screening of viral host range mutants exemplified by discovery of SAMD9 and WDR6 as inhibitors of the vaccinia virus K1L-C7L- mutant. MBio 6, 10.1128/mbio.01122-01115 (2015).
Hou, G. et al. SAMD9 senses cytosolic double-stranded nucleic acids in epithelial and mesenchymal cells to induce antiviral immunity. Nature communications 16, 3756 (2025).
Legrand, A. et al. Evolutionary characterization of antiviral SAMD9/9L across kingdoms supports ancient convergence and lineage-specific adaptations. Nature Ecology & Evolution 9, 2206–2222 (2025).
Legrand, A. et al. SAMD9L acts as an antiviral factor against HIV-1 and primate lentiviruses by restricting viral and cellular translation. PLoS biology 22, e3002696 (2024).
Cannac, M. et al. SAMD9L inhibits flavivirus translation independently of its capacity to trigger innate immune response. PLoS Pathogens 21, e1013773 (2025).
Narumi, S. et al. SAMD9 mutations cause a novel multisystem disorder, MIRAGE syndrome, and are associated with loss of chromosome 7. Nature genetics 48, 792–797 (2016).
Buonocore, F. et al. Somatic mutations and progressive monosomy modify SAMD9-related phenotypes in humans. The Journal of clinical investigation 127, 1700–1713 (2017).
Chen, D.-H. et al. Ataxia-pancytopenia syndrome is caused by missense mutations in SAMD9L. The American Journal of Human Genetics 98, 1146–1158 (2016).
Tesi, B. et al. Gain-of-function SAMD9L mutations cause a syndrome of cytopenia, immunodeficiency, MDS, and neurological symptoms. Blood, The Journal of the American Society of Hematology 129, 2266–2279 (2017).
Schwartz, J.R. et al. The genomic landscape of pediatric myelodysplastic syndromes. Nature communications 8, 1557 (2017).
Wong, J.C. et al. Germline SAMD9 and SAMD9L mutations are associated with extensive genetic evolution and diverse hematologic outcomes. JCI insight 3, e121086 (2018).
Knight, M.J., Leettola, C., Gingery, M., Li, H. & Bowie, J.U. A human sterile alpha motif domain polymerizome. Protein Science 20, 1697–1706 (2011).
Peng, S. et al. Structure and function of an effector domain in antiviral factors and tumor suppressors SAMD9 and SAMD9L. Proceedings of the National Academy of Sciences 119, e2116550119 (2022).
Holm, L. Dali server: structural unification of protein families. Nucleic acids research 50, W210–W215 (2022).
Zhao, K., Chai, X. & Marmorstein, R. Structure of the yeast Hst2 protein deacetylase in ternary complex with 2′-O-acetyl ADP ribose and histone peptide. Structure 11, 1403–1411 (2003).
Alfieri, C., Chang, L. & Barford, D. Mechanism for remodelling of the cell cycle checkpoint protein MAD2 by the ATPase TRIP13. Nature 559, 274–278 (2018).
Roy, M.J. et al. Structural mapping of PEAK pseudokinase interactions identifies 14-3-3 as a molecular switch for PEAK3 signaling. Nature communications 14, 3542 (2023).
Yang, X.-J. et al. Crystal structure of a Y-box binding protein 1 (YB-1)-RNA complex reveals key features and residues interacting with RNA. Journal of Biological Chemistry 294, 10998–11010 (2019).
Bravo, J.P., Ramos, D.A., Fregoso Ocampo, R., Ingram, C. & Taylor, D.W. Plasmid targeting and destruction by the DdmDE bacterial defence system. Nature 630, 961–967 (2024).
Loeff, L. et al. Molecular mechanism of plasmid elimination by the DdmDE defense system. Science 385, 188–194 (2024).
Wang, Y., Tian, Y., Yang, X., Yu, F. & Zheng, J. Filamentation activates bacterial Avs5 antiviral protein. Nature Communications 16, 2408 (2025).
Muralidharan, A. et al. Molecular basis for anti-jumbo phage immunity by AVAST Type 5. Molecular Cell 86, 740–756.e749 (2026).
Maekawa, S., Ohto, U., Shibata, T., Miyake, K. & Shimizu, T. Crystal structure of NOD2 and its implications in human disease. Nature communications 7, 11813 (2016).
Sahoo, S.S. et al. Clinical evolution, genetic landscape and trajectories of clonal hematopoiesis in SAMD9/SAMD9L syndromes. Nature medicine 27, 1806–1817 (2021).
Sahoo, S.S., Erlacher, M. & Wlodarski, M.W. Genetic and clinical spectrum of SAMD9 and SAMD9L syndromes: from variant interpretation to patient management. Blood 145, 475–485 (2025).
Sharif, H. et al. Structural mechanism for NEK7-licensed activation of NLRP3 inflammasome. Nature 570, 338–343 (2019).
Hochheiser, I.V. et al. Structure of the NLRP3 decamer bound to the cytokine release inhibitor CRID3. Nature 604, 184–189 (2022).
Xiao, L., Magupalli, V.G. & Wu, H. Cryo-EM structures of the active NLRP3 inflammasome disc. Nature 613, 595–600 (2023).
Kim, C.A., Gingery, M., Pilpa, R.M. & Bowie, J.U. The SAM domain of polyhomeotic forms a helical polymer. Nature structural biology 9, 453–457 (2002).
Baron, M.K. et al. An architectural framework that may lie at the core of the postsynaptic density. Science 311, 531–535 (2006).
Thanos, C.D., Goodwill, K.E. & Bowie, J.U. Oligomeric structure of the human EphB2 receptor SAM domain. Science 283, 833–836 (1999).
Mastronarde, D.N. Automated electron microscope tomography using robust prediction of specimen movements. Journal of structural biology 152, 36–51 (2005).
Punjani, A., Rubinstein, J.L., Fleet, D.J. & Brubaker, M.A. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat Methods 14, 290–296 (2017). https://doi.org/10.1038/nmeth.4169
Bepler, T. et al. Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs. Nature methods 16, 1153–1160 (2019).
Abramson, J. et al. Accurate structure prediction of biomolecular interactions with AlphaFold 3. Nature 630, 493–500 (2024). https://doi.org/10.1038/s41586-024-07487-w
Pettersen, E.F. et al. UCSF ChimeraX: Structure visualization for researchers, educators, and developers. Protein Sci 30, 70–82 (2021). https://doi.org/10.1002/pro.3943
Casanal, A., Lohkamp, B. & Emsley, P. Current developments in Coot for macromolecular model building of Electron Cryo-microscopy and Crystallographic Data. Protein Sci 29, 1069–1078 (2020). https://doi.org/10.1002/pro.3791
Afonine, P.V. et al. Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Crystallogr D Struct Biol 74, 531–544 (2018). https://doi.org/10.1107/S2059798318006551
Williams, C.J. et al. MolProbity: more and better reference data for improved all-atom structure validation. Protein science 27, 293–315 (2018).
指标
DOI：
Submission ID：
下载次数
已发布
如何引用
下载引用
利益冲突声明
作者声明无任何需要披露的利益冲突。
Copyright
本预印本的版权持有者为作者/资助方。
This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.